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[ape.git] / R / read.nexus.R

diff --git a/R/read.nexus.R b/R/read.nexus.R
index 54384561166cad5e3e272b36cc01d7e23a70bb3e..3edcd3f5903b610f42edce93884ad2665cb640a0 100644 (file)
--- a/R/read.nexus.R
+++ b/R/read.nexus.R
@@ -1,8 +1,8 @@
-## read.nexus.R (2008-07-04)
+## read.nexus.R (2009-04-01)
 
 ##   Read Tree File in Nexus Format
 
-## Copyright 2003-2008 Emmanuel Paradis
+## Copyright 2003-2009 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
@@ -110,7 +110,7 @@ read.nexus <- function(file, tree.names = NULL)
         if (any(w)) { # in case all comments use at least 2 lines
             s <- LEFT[w]
             X[s] <- gsub("\\[[^]]*\\]", "", X[s])
-            ## The previous regexp was quite tough to find: it makes
+            ## The above regexp was quite tough to find: it makes
             ## possible to delete series of comments on the same line:
             ##       ...[...]xxx[...]...
             ## without deleting the "xxx". This regexp is in three parts:
@@ -153,16 +153,25 @@ read.nexus <- function(file, tree.names = NULL)
     tree <- X[start:end]
     rm(X)
     tree <- gsub("^.*= *", "", tree)
+    ## check whether there are empty lines from the above manips:
+    tree <- tree[tree != ""]
     semico <- grep(";", tree)
     Ntree <- length(semico)
     ## are some trees on several lines?
-    if (any(diff(semico) != 1)) {
-        STRING <- character(Ntree)
-        s <- c(1, semico[-Ntree] + 1)
-        j <- mapply(":", s, semico)
-        for (i in 1:Ntree)
-            STRING[i] <- paste(tree[j[, i]], collapse = "")
-    } else STRING <- tree
+    if (Ntree == 1 && length(tree) > 1) STRING <- paste(tree, collapse = "") else {
+        if (any(diff(semico) != 1)) {
+            STRING <- character(Ntree)
+            s <- c(1, semico[-Ntree] + 1)
+            j <- mapply(":", s, semico)
+            if (is.list(j)) {
+                for (i in 1:Ntree)
+                    STRING[i] <- paste(tree[j[[i]]], collapse = "")
+            } else {
+                for (i in 1:Ntree)
+                    STRING[i] <- paste(tree[j[, i]], collapse = "")
+            }
+        } else STRING <- tree
+    }
     rm(tree)
     STRING <- gsub(" ", "", STRING)
     colon <- grep(":", STRING)
@@ -208,14 +217,19 @@ read.nexus <- function(file, tree.names = NULL)
     }
     if (Ntree == 1) {
         trees <- trees[[1]]
-        if (translation) trees$tip.label <- TRANS[, 2]
+        if (translation) {
+            trees$tip.label <-
+                if (length(colon)) TRANS[, 2] else
+                TRANS[, 2][as.numeric(trees$tip.label)]
+        }
     } else {
         if (!is.null(tree.names)) names(trees) <- tree.names
         if (translation) attr(trees, "TipLabel") <- TRANS[, 2]
         class(trees) <- "multiPhylo"
     }
     if (length(grep("[\\/]", file)) == 1)
-        file <- paste(getwd(), file, sep = "/")
+        if (!file.exists(file)) # suggestion by Francois Michonneau
+            file <- paste(getwd(), file, sep = "/")
     attr(trees, "origin") <- file
     trees
 }